Your Abyssal Ruins theory assumes that there was no king in ancient times and that the story is a prophecy about Reshiram and Zekrom one day being split. Certainly, this is possible, but when we start accounting for a universe split, we should remember that the Abyssal Ruins' text changes depending on the universe (version). More importantly, whoever wrote the messages definitely wanted the prophecy to come true judging by their reverence toward the king. So I would say that under the prophecy assumption, the Abyssal Ruins civilization did not try to prevent the split at all, and in a way they caused the split by writing down not one prophecy but two.
Perhaps the Puzzle Cube is indeed an elaborate Time Capsule that will make it possible for the Original Dragon to exist despite the split. Since it doesn't seem that
Kyurem will actually fuse with either Reshiram or Zekrom, I have doubts that the split can be undone. The Puzzle Cube may be the only way to bring forth the original dragon (by projecting its past image), at least in these games.
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